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Size: 29114
Comment: sage-4.4.4 porting effort abandoned.
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Size: 25188
Comment: Fix invocation. atlas, readline & pari fixes have been integrated into Sage. Add cephes and flintqs issues
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| = Sage FreeBSD 8.x build notes for Sage 4.4.4 = | = Sage FreeBSD 8.x build notes for Sage 4.5 = |
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| * Install ports/shells/bash or ports/shells/bash3 (I used 4.1.5) | * Install ports/shells/bash or ports/shells/bash3 (I used 4.1.7) |
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| FreeBSD 7.x hasn't been tested with Sage 4.4.4 but is expected to work. * Unpack sage-4.4.4.tar * `cd sage-4.4.4` * Unpack [[attachment:sage-4.4.4.patch]] which includes the following: |
FreeBSD 7.x hasn't been tested with Sage 4.5 but is expected to work. * Unpack sage-4.5.tar * `cd sage-4.5` * Unpack [[attachment:sage-4.5.patch]] which includes the following: |
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| . `SAGE_PORT=yes SAGE_FORTRAN=/usr/local/bin/gfortran45 SAGE_FORTRAN_LIB=/usr/local/lib/gcc45/libgfortran.so gmake` Note that there are currently issues with using gcc45/g++45 to build Sage - configuration errors in the FreeBSD port of gcc45 means that the wrong shared libraries get used by default. See http://www.freebsd.org/cgi/query-pr.cgi?pr=129518 |
. `LD_LIBRARY_PATH=/usr/local/lib/gcc45 SAGE_PORT=yes SAGE_FORTRAN=/usr/local/bin/gfortran45 SAGE_FORTRAN_LIB=/usr/local/lib/gcc45/libgfortran.so gmake` Note that the LD_LIBRARY_PATH is needed to work arounf configuration errors in the FreeBSD port of gcc45 - see http://www.freebsd.org/cgi/query-pr.cgi?pr=129518 |
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| * The patch to standard/deps ensures that bash is used. By default, gmake will use /bin/sh to execute commands and the patched line sources local/bin/sage-env - which includes the bash'ism 'source' instead of '.'. Whilst that file begins with a #! line invoking bash, because it must be sourced, it will actually execute in the invoking shell. === atlas-3.8.3.p12 === Various fixes to make it compile on FreeBSD * FreeBSD uses an '_fbsd' suffix on the ELF format supported by `ld` - prevents `ld: unrecognised emulation mode: elf_x86_64` error during atlas build. Reported upstream as https://sourceforge.net/tracker/index.php?func=detail&aid=2728930&group_id=23725&atid=379482 {{{#!wiki comment * Treat shared libraries the same as Linux - otherwise they aren't correctly detected by (eg) numpy. (sage-specific) Trac ticket: [[http://trac.sagemath.org/sage_trac/ticket/7827|#7827]] * `sysctl` is not in the default user path so use an explicit pathname (optional) * The newer AMD CPUs all identify as 'Athlon' so use the existence of multiple cores to distinguish between K7 (i386) and later (Hammer) CPUs. (optional) * Correct various sysctl OIDs to match the names FreeBSD uses. (optional) This and previous two reported upstream as https://sourceforge.net/tracker/?func=detail&atid=379483&aid=2728927&group_id=23725 * Building the `libclapack.so` should result in a `libclapack.so` being created. This appears to be a copy-and-paste error in atlas and has been reported as https://sourceforge.net/tracker/?func=detail&atid=379483&aid=2728935&group_id=23725 (Note that this is not relevant to sage as libclapack is not built or used). * numpy on FreeBSD expects atlas to build different and (according to the FreeBSD numpy port, static) threaded libraries: libatlas_r instead of libatlas and libalapack_r instead of liblapack. libatlas_r is built as part of the threaded version of atlas. libalapack_r is a FreeBSD special which explicitly combines all of liblapack from the atlas lapack build with the threaded atlas version of liblapack. numpy error from last point above: {#{{ atlas_blas_info: libraries f77blas,cblas,atlas_r not found in /usr/home/peter/sage-4.1/local/lib NOT AVAILABLE /usr/home/peter/sage-4.1/spkg/build/numpy-1.3.0.p0/src/numpy/distutils/system_info.py:1383: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) ... atlas_info: libraries f77blas,cblas,atlas_r not found in /usr/home/peter/sage-4.1/local/lib libraries lapack_atlas not found in /usr/home/peter/sage-4.1/local/lib numpy.distutils.system_info.atlas_info NOT AVAILABLE /usr/home/peter/sage-4.1/spkg/build/numpy-1.3.0.p0/src/numpy/distutils/system_info.py:1290: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) ... }}} |
=== cephes-2.8 === * FreeBSD does not yet include a full C99 libm so enable cephes on FreeBSD. * Correct error in the patched c9x-complex/makefile that refers to non-existent test sources. * Enable '-e' option on spkg-install to catch errors Trac ticket: [[http://trac.sagemath.org/sage_trac/ticket/TBA|#TBA]] |
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| === flintqs-20070817.p5 === `TonelliShanks.h` references `int32_t` but does not directly include `<stdint.h>`. On FreeBSD using gcc45 (but not the base gcc), this causes compilation to fail with: {{{ g++ -ansi -c TonelliShanks.cpp -o TonelliShanks.o -I/tank/obj/sage/sage-4.5/local/include -Wall -Wno-sign-compare -fomit-frame-pointer -O2 In file included from TonelliShanks.cpp:31:0: TonelliShanks.h:41:8: error: 'int32_t' does not name a type TonelliShanks.h:43:51: error: 'int32_t' has not been declared TonelliShanks.cpp:67:1: error: 'int32_t' does not name a type TonelliShanks.cpp:136:54: error: 'int32_t' has not been declared TonelliShanks.cpp: In function 'void sqrtmodpk(__mpz_struct*, __mpz_struct*, __mpz_struct*, __mpz_struct*, int)': TonelliShanks.cpp:140:11: error: 'int32_t' was not declared in this scope TonelliShanks.cpp:140:19: error: expected ';' before 'i' TonelliShanks.cpp:140:25: error: 'i' was not declared in this scope make[2]: *** [TonelliShanks.o] Error 1 make[2]: Leaving directory `/tank/obj/sage/sage-4.5/spkg/build/flintqs-20070817.p5/src' Error building William Hart's Quadratic Sieve }}} As a work-around, make `TonelliShanks.h` idempotent on FreeBSD (it probably should be on all architectures but making the patch FreeBSD-specific simplifies testing). Trac ticket: [[http://trac.sagemath.org/sage_trac/ticket/?|#?]] |
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| === matplotlib-0.99.1.p4 === | === matplotlib-0.99.3 === |
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| === pari-2.3.5.p1 === FreeBSD refers to the x86_64 architecture under its original name of 'amd64' so use this as an alias for x86_64. The `-fPIC' fix is needed to correct: {{{ gcc -o libpari-gmp.so.2.3.3 -shared -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer -Wl,-shared,-soname=libpari-gmp.so.2 mp.o mpinl.o Flx.o Qfb.o RgX.o alglin1.o alglin2.o arith1.o arith2.o base1.o base2.o base3.o base4.o base5.o bibli1.o bibli2.o buch1.o buch2.o buch3.o buch4.o galconj.o gen1.o gen2.o gen3.o ifactor1.o perm.o polarit1.o polarit2.o polarit3.o rootpol.o subcyclo.o subgroup.o trans1.o trans2.o trans3.o anal.o compat.o default.o errmsg.o es.o init.o intnum.o members.o sumiter.o aprcl.o elldata.o elliptic.o galois.o groupid.o kummer.o mpqs.o nffactor.o part.o stark.o subfield.o thue.o -lc -lm -L/home/peter/sage/sage-4.4.4/local/lib -lgmp /usr/bin/ld: mp.o: relocation R_X86_64_32S can not be used when making a shared object; recompile with -fPIC mp.o: could not read symbols: Bad value *** Error code 1 Stop in /home/peter/sage/sage-4.4.4/spkg/build/pari-2.3.3.p5/src/Ofreebsd-amd64. }}} Trac ticket: [[http://trac.sagemath.org/sage_trac/ticket/7825|#7825]] Reported upstream as http://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=1022 |
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| === readline-6.0.p1 === readline-6.0.p1/spkg-install contains a typo in some FreeBSD-specific code, leading to the following error: {{{ ... /bin/sh ../support/shlib-install -O freebsd8.0 -d /home/peter/sage/sage-4.4.4/local/lib -b /home/peter/sage/sage-4.4.4/local/bin -i "/usr/bin/install -c -m 644" libreadline.so.6.0 install: you may need to run ldconfig make[1]: Leaving directory `/home/peter/sage/sage-4.4.4/spkg/build/readline-6.0.p1/src/shlib' ln: SAGE_LOCAL/lib/libreadline.so: No such file or directory }}} The affected code is no longer required with readline-6.0 so delete it. FreeBSD 3.x and later default to ELF, rather then a.out. A utility objformat(1) was temporarily introduced to enable third-party applications to determine te object format. This has now been deleted and code should assume ELF format if it does not exist. Explicitly linking libreadline against libtermcap is necessary to ensure that dependencies are picked up. Trac ticket [[http://trac.sagemath.org/sage_trac/ticket/7821|#7821]] === sage-4.4.4 === |
=== sage-4.5 === |
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| === sage_scripts-4.4.4 === | === sage_scripts-4.5 === |
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| === singular-3.1.0.4.p6 === | === singular-3.1.0.4.p7 === |
Sage FreeBSD 8.x build notes for Sage 4.5
Note that this is a work-in-progress and not currently complete
Contents
Contents
Overall build environment differences
sh and /bin/sh are a POSIX shell, rather than bash.
make is the BSD make, not GNU make
Preparatory work
- Install ports/shells/bash or ports/shells/bash3 (I used 4.1.7)
- Install ports/devel/gmake
- Install ports/lang/gcc45 - FreeBSD no longer ships with a Fortran compiler by default.
- Install ports/devel/autoconf262
- Install ports/converters/libiconv
Ensure POSIX semaphores are available. This is required for ecl (at least). These are not available by default before FreeBSD 7.3 or 8.0 and should be enabled by either kldload sem or building a kernel with options P1003_1B_SEMAPHORES. If they are not available, building ecl will fail with Bad system call.
It's possible there are other dependencies, I haven't tried building sage in a clean (tinderbox) environment.
Building Sage
On FreeBSD 8.x
FreeBSD 7.x hasn't been tested with Sage 4.5 but is expected to work.
- Unpack sage-4.5.tar
cd sage-4.5
Unpack sage-4.5.patch which includes the following:
- Create symlinks to mask name differences.
ln -s /usr/local/bin/gmake local/bin/make
ln -s /usr/local/bin/bash local/bin/sh
ln -s /usr/local/bin/gfortran45 local/bin/gfortran
Various patches as described below into spkg/patches
- Build Sage
LD_LIBRARY_PATH=/usr/local/lib/gcc45 SAGE_PORT=yes SAGE_FORTRAN=/usr/local/bin/gfortran45 SAGE_FORTRAN_LIB=/usr/local/lib/gcc45/libgfortran.so gmake
Note that the LD_LIBRARY_PATH is needed to work arounf configuration errors in the FreeBSD port of gcc45 - see http://www.freebsd.org/cgi/query-pr.cgi?pr=129518
The gmake to make symlink is necessary to compile (eg) eclib - which is documented as requiring GNU make, and has this symlink as a suggested workaround.
Current Status
Currently, the following tests fail on FreeBSD 8.1-PRERELEASE/amd64. Full logs at sage-4.4.4.freebsd8.1-amd64.test.log.
The actual failures indicate that the port still needs significant work and include:
- Failed coercions in coercion.rst
- python/site-packages/sage/rings/polynomial/pbori.so runtime linking against the wrong C++ library.
- Invalid polymonials reported by scheme.py
- FreeBSD memory usage patch is incomplete
Notes on spkgs and attached patches
base.patch
- The patch to base/sage-spkg enables the local patching that the rest of the patches rely on. Note that this patch is not intended to be merged into sage but provides a convenient mechanism to apply local patches without requiring that the spkg files are locally re-rolled.
cephes-2.8
- FreeBSD does not yet include a full C99 libm so enable cephes on FreeBSD.
- Correct error in the patched c9x-complex/makefile that refers to non-existent test sources.
- Enable '-e' option on spkg-install to catch errors
Trac ticket: #TBA
flintqs-20070817.p5
TonelliShanks.h references int32_t but does not directly include <stdint.h>. On FreeBSD using gcc45 (but not the base gcc), this causes compilation to fail with:
g++ -ansi -c TonelliShanks.cpp -o TonelliShanks.o -I/tank/obj/sage/sage-4.5/local/include -Wall -Wno-sign-compare -fomit-frame-pointer -O2 In file included from TonelliShanks.cpp:31:0: TonelliShanks.h:41:8: error: 'int32_t' does not name a type TonelliShanks.h:43:51: error: 'int32_t' has not been declared TonelliShanks.cpp:67:1: error: 'int32_t' does not name a type TonelliShanks.cpp:136:54: error: 'int32_t' has not been declared TonelliShanks.cpp: In function 'void sqrtmodpk(__mpz_struct*, __mpz_struct*, __mpz_struct*, __mpz_struct*, int)': TonelliShanks.cpp:140:11: error: 'int32_t' was not declared in this scope TonelliShanks.cpp:140:19: error: expected ';' before 'i' TonelliShanks.cpp:140:25: error: 'i' was not declared in this scope make[2]: *** [TonelliShanks.o] Error 1 make[2]: Leaving directory `/tank/obj/sage/sage-4.5/spkg/build/flintqs-20070817.p5/src' Error building William Hart's Quadratic Sieve
As a work-around, make TonelliShanks.h idempotent on FreeBSD (it probably should be on all architectures but making the patch FreeBSD-specific simplifies testing).
Trac ticket: #?
matplotlib-0.99.3
Add support for FreeBSD later than 6.x. Otherwise you get :
BUILDING MATPLOTLIB
matplotlib: 0.99.1
python: 2.6.2 (r262:71600, Jan 3 2010, 12:58:40) [GCC
4.2.1 20070719 [FreeBSD]]
platform: freebsd8
REQUIRED DEPENDENCIES
Traceback (most recent call last):
File "setup.py", line 123, in <module>
if not check_for_numpy():
File "/home/peter/sage/sage-4.4.4/spkg/build/matplotlib-0.99.1.p2/src/setupext.py", line 506, in check_for_numpy
add_base_flags(module)
File "/home/peter/sage/sage-4.4.4/spkg/build/matplotlib-0.99.1.p2/src/setupext.py", line 327, in add_base_flags
[os.path.join(p, 'include') for p in basedir[sys.platform] ])
KeyError: 'freebsd8'Trac #5873 Reported upstream as https://sourceforge.net/tracker/?func=detail&aid=3031051&group_id=80706&atid=560722
numpy-1.3.0.p3
__init__.py needs a sage-specific patch to prefer sage_fortran on FreeBSD. This is necessary to prevent matplotlib dying with:
BUILDING MATPLOTLIB
matplotlib: 0.99.1
python: 2.6.2 (r262:71600, Jan 3 2010, 12:58:40) [GCC
4.2.1 20070719 [FreeBSD]]
platform: freebsd8
REQUIRED DEPENDENCIES
numpy: no
* You must install numpy 1.1 or later to build
* matplotlib.By default, numpy references threaded atlas libraries, as well as a custom variant on the lapack library, on FreeBSD. The reasoning behind this is unclear - there is nothing in the numpy documentation to indicate whether a threaded or non-threaded atlas is needed and the publicly available SVN logs do not mention this code. A query to the numpy mailing list elicited a response that either threaded or non-threaded atlas can be used and suggesting that the special-casing for FreeBSD may be obsolete. By default, atlas is built non-threaded and r-2.6.1.p23 assumes a non-threaded atlas and fails when only the threaded libraries are installed. Based on this, the special casing for FreeBSD was removed from numpy - it now uses the same libraries irrespective of the host OS.
Trac ticket: #7831
sage-4.5
Compiling sage/combinat/partitions_c.cc fails because FreeBSD 7.x does not define sqrtl (it was introduced in FreeBSD 8.0). As a hackish workaround, define sqrtl to be sqrt on older versions of FreeBSD.
- FreeBSD does not include a definition for log2() in libm. Use a simplistic definition of log2(x) = log2(e) * ln(x) - this is numerically poor but can be cleaned up later if required.
sage/groups/perm_gps/permgroup_element.c fails to compile because LONG_LONG_MAX is not available on FreeBSD. Some googling suggests that this macro is either a GNU extension or is deprecated in C99 and has been replaced by LLONG_MAX - I have not been able to find a direct reference but indirect references include the following links: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=168346#19 http://linux.softpedia.com/progChangelog/GNU-ddrescue-Changelog-6106.html http://clang.llvm.org/doxygen/limits_8h-source.html
Remaining issues include:
sage/symbolic/pynac.cpp fails to compile because FreeBSD libm is mostly missing long double functions - specifically tgammal() and lgammal() in this case.
Trac ticket: #?
sage_scripts-4.5
Patch sage-spkg to apply local patches. This patch also disables deletion of the spkg/build/FOO temporary directories - which was useful during porting. This latter patch can be safely removed.
singular-3.1.0.4.p7
By default, you get the following, which is corrected by the patch to singuname.sh:
make[2]: Entering directory `/home/peter/sage/sage-4.4.4/spkg/build/singular-3-1-0-4-20090818.p2/src' make[2]: *** No rule to make target `distclean'. Stop. make[2]: Leaving directory `/home/peter/sage/sage-4.4.4/spkg/build/singular-3-1-0-4-20090818.p2/src' rm: /home/peter/sage/sage-4.4.4/local/bin/Singular*: No such file or directory creating cache ./config.cache checking uname for singular... unknown configure: error: Unknown architecture: Check singuname.sh Unable to configure Singular.
Correct configure script for amd64 by patching the autoconf inputs and re-running autoconf. This corrects a problem where linking libsingular.so reports lots of undefined references to both internal om* functions and functions within libncurses.
Several other trivial fixes to support dynamic linking on FreeBSD/amd64.
Trac ticket: #7832